Deform Mesh Subtly, randomly across many Objects
A few side comments.

You don't need very high subdivisions for such a simple shape.
You don't need to apply the subdivision
You don't need to Transform &gt; To Sphere, you can use a Cast modifier.

To address you main question, if you want to add subtle variations to your objects your answer lies in a Displace modifier.
Now if you just add one to your M&amp;Ms and duplicate them they will all have the same deformation and remain identical.
The trick here is to change the Texture Coordinates for your displace texture to Global so the texture is mapped using scenes world coordinate space, giving the impression of randomness across several objects.
Have in mind that this method is unsuited if you want to animate the objects, since the shape would wiggle around as you move them. You also cannot link as group/collection libraries since the coordinate considered for displacement is always read from the same static point in space the original was defined, not where each individual instance is placed at.